Soul Eater is my number 1 candidate for a reboot. The show went to shit imo when it deviated from the manga. I'm going to be honest, if they made a Soul Eater remake, I think it could end up being better than FMA:B.
Angel Beats! was poorly done, and if they remade it and cleaned it up a bit, I think it would be amazing. But, that won't happen because 1-cour shows never get reboots.

Too many anime need another season. But, my top picks would be Haganai, Spice and Wolf, WataMote, Attack on Titan, Chu2, NouCome, HenNeko, Sunday Without God, Seitokai Yakuindomo, Kawaisou, and Squid Girl. Like I said, way too many, and I'd be lucky if 3 of these even got another season.

While I am enjoying the current anime of Tokyo Ghoul I'd be lying my ass off if I didn't nominate it for a reboot. Preferably anime that followed the manga exactly regardless of what the anime only viewer would think. I state it that way because that's the reason why they switched the second and third arcs around.

1. Akira: I'd love to see this as a proper series that could follow the manga and flesh out the storyline more.
2. Great Teacher Onizuka: A reboot of this that goes right through to the end of the manga would be awesome.